Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30082 discussions

Defining ROI and Finding the Cortical Thickness
by Mahtab Farahbakhsh 19 May '16

19 May '16

Dear freeSurfer, I have problems with defining new labels for my brain scan or even of fsaverage. I need to define a new label (ROI) to be able to find the grey matter thickness for that specific region. My first problem is that when I define a new label on fsaverage, it does not save it for me and it gives me the following error: mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz, -1): could not open file /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could not open label file /Applications/freesurfer/subjects/fsaverage/label/ROI_test.label I intend to define a new label (ROI) on fsaverage and then use the mri_labe2label command to copy it on my desired structural MRI image. But it does not work for me. My second problem is that when I define a new label on my subject's MRI image and I run the mri_anatomical_stats with the label of my subject, it does not give me any output and this is what I get: bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh limiting computations to label anon/label/lh.test.label. reading volume /Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz... reading input surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white... reading input pial surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial... reading input white surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white... and the error is that it could not find the file lh.test.label, however I can see it in the label folder. Please guide me with this issue. Best Regards, Mahtab.

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Neuroimaging position available
by Anders Martin Fjell 19 May '16

19 May '16

At the Research Group for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available position in neuroimaging for an excellent candidate, who will work with several projects on life-span development and aging, dementia and biomedical risk factors using different brain imaging modalities. Please find more info here: http://uio.easycruit.com/vacancy/1633291/65775?iso=no Interested candidates are welcome to contact me if they have questions. Best whishes, Anders M Fjell http://www.oslobrains.no

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Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 18 May '16

18 May '16

Hi Doug, Sorry- I've added entire correspondence onto the end of this e-mail. I don't think the disk filled up as I am on a 3 TB hard drive and I still have ~2 TB of free space on my disk. Anything else you think it could be? Thanks! Joseph Aloi Please remember to include previous correspondence otherwise we can't keep track of the problem! Eg, I don't have the previous email to see what the error was. Is it possible that the disk filled up? On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > Hi Doug, > > Yes, you are correct- data I have previously processed without any > problems is no longer being processed. > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > ago so I have not changed my freesurfer version recently. > > Thanks! > > Joseph Aloi > Graduate Student, MD/PhD Scholars Program > Department of Pharmacology and Experimental Neuroscience > University of Nebraska Medical Center > > Neurobehavioral Research Assistant, Center For Neurobehavioral Research > Boys Town National Research Hospital So the exact same data set is now generating an error whereas it ran smoothly before? What version of FS are you using? Did you change versions? doug On 05/16/2016 09:49 AM, Aloi, Joseph wrote: > > Hi freesurfer experts, > > I have recently begun to use freesurfer to do structural MRI > analyses. I have been able to successfully process about 40 > structural scans with recon-all thus far, but starting a few days ago, > I started getting this error whenever I run recon-all: > > WARNING: file > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not > contain a Siemens ASCII header > > has this file been anonymized? > > ERROR: cannot unpack mosiacs without ASCII header > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 > > recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 CDT 2016 > > Here are a few of the troubleshooting steps I’ve tried to track down > the cause of the error: > > -- Re-run recon-all with a couple of scans from my dataset that I have > already successfully processed > > - - Re-run recon-all the same datasets but on a different computer > > - - Re-convert the scans from .ima files to dicoms in osirix, then > run recon-all > > > For all of these steps, I have gotten the exact same error message. > The files should be anonymized, since I used osirix’s “anonymize and > convert” function to generate the dicom files (the scans were given to > me as .ima files). > > Any suggestions on what to try next? > > Thank you! > > > Joseph Aloi > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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FreeSurfer Validation and Longitudinal Analysis of WM Hyperintensities
by Navena Rebecca Lingum 18 May '16

18 May '16

Dear FreeSurfer experts, My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command? Navena Lingum

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3T flag
by Kasper Jessen 18 May '16

18 May '16

Dear FreeSurfer group, Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment. However, where can i find the documentation for the above? Best regards, Kasper

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T2pial and [LONG]
by Kasper Jessen 18 May '16

18 May '16

Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface. Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces? Best regards, Kasper Jessen

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Same coordinates for all labels
by Nabin Koirala 18 May '16

18 May '16

Dear FS team, I am trying to find the centroid using mri_surfcluster using the following command but I am getting the same coordinate for all labels. I couldn't quiet understand what's wrong. Your suggestion would be really appreciated. NOTE: The coordinates differs for hemisphere. mri_surfcluster --in ./S/surf/rh.thickness --clabel ./S/centroid/rh.frontalpole.label --sum ./S/centroid/sum.rh.6.label --centroid --thmin 0 --hemi rh --subject S Thank you. Regards, Nabin

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Question on Yeo 2015 cognitive atlas
by Josh Gray 17 May '16

17 May '16

Hello, I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website). Is there a quick way to do this? Thank you, Josh Gray -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia

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Re: [Freesurfer] Freesurfer (white/grey matter changes)
by Limachia, Gaurang (NIH/NINDS) [F] 17 May '16

17 May '16

This is how the white matter changes look like after making corrections and running recon all. From: "Limachia , Gaurang (NIH/NINDS) [F]" <gaurang.limachia(a)nih.gov<mailto:gaurang.limachia@nih.gov>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, May 17, 2016 at 4:49 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Freesurfer I made the necessary changes to the white matter, and when I ran recon all the changes with the voxels showed up, but there was no change to the contour lines. In order to change the gray matter volume, I can¹t find the changes I already made on the white matter (the picture with green control points). If I am able to see the changes I made to the white matter, I can utilize the control points to modify the segmentation. Also will this impact the gray matter volume as well as per your previous response to my question. Thanks, Gaurang

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Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill
by gangli 17 May '16

17 May '16

Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic and critical early brain development in both health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu <https://outlook.unc.edu/owa/redir.aspx?SURL=r-ilRGXKGkv6jOyzGz3FjAPbDG9VNfM…> ). For more information, please visit: http://www.unc.edu/~gangl/contact.html <https://outlook.unc.edu/owa/redir.aspx?SURL=HcVZFV_dUot9RdWseT8XGNDO-UYKJHN…> .

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